The advantage of animation is that you can do some really cool-looking alien environments, some amazing space shots, and just get a really futuristic atmosphere. The reality of animation on a TV budget is that the characters would have to be stylized, which is my only real concern, but I don't think there's any inherent reason they couldn't do both stylized yet not too crazy proportionally. Actually, the ST:FF characters don't look too bad if they could render something like that in CG. I think Batman: TAS did a great job there, in the traditional animated world, at least.Don't knock animation cause it's animation. It's a lot more freeing than live action, and you can tell just as serious stories as you can in liveaction.
I wouldn't mind a Clone Wars style for Star Trek. The characters are stylized, but still recognizable. Toss in some really great writing backing some solid story concepts. In fact, the Clone Wars production tream would be my dream team for a ST animation.